Food loss, resource leaks, waste generation and negative impacts on the environment are some of the damages favored by the linear economy, due to this a transition to the circular economy is sought which seeks to take advantage of food by-products and waste, promoting their reuse or transformation into high added value products, being of greater interest fibers with prebiotic properties, immunostimulant polysaccharides, as well as peptides and organic compounds with antimicrobial, antifungal and antioxidant activity. To obtain them, technological processes are required that allow for their recovery and improvement of performance, while also employing methods that enable them to remain stable or enhance their activity in various systems. Additionally, the integration of nanotechnology is highlighted as a key tool in the valorization of bioactive compounds derived from agro-industrial waste. Through its application in nanoformulations—such as nanoparticles, nanoemulsions, or bioactive coatings—it is possible to enhance the stability, bioavailability, and functionality of these compounds, thereby expanding their applications across the food, pharmaceutical, and environmental sectors. This technological convergence strengthens the objectives of the circular economy by optimizing resource use and minimizing environmental impact. Therefore, in this chapter, the main bioactives of interest in the food industry are presented, along with the conventional methods of obtaining them and the formulation processes for their use. Additionally, the use of Ganoderma resinaceum CS27 as an alternative to agro-industrial waste in the lignocellulose biorefinery system is discussed.